the online method of booking is entirely automated and costs bugger all once the system has been developed!
To say a system costs "bugger all" once developed is a bit of an understatement to say the least.
Whether the charges passed on are reflective of actual costs is another matter altogether and one that would have to be evaluated on a case by case basis.
However, a properly run e-commerce website will be subject to a multitude of costs.
One simple example that you as a consumer can easily relate to is the fact that credit card bookings will attract a processing fee on the seller's merchant account (the value of which varies depending on what card is used and which payment processor the seller uses to settle credit card payments, but there will always be a fee payable).... 3.5% + 15p per transaction is just one example of many I could quote, but obviously busy sites will have negotiated slightly better commercials.
There are also other back-end related items you can't relate so easily to, such as ongoing development costs, infrastructure, internet connectivity, penetration testing etc. etc. etc. etc. etc. etc.
How these costs get passed on will depend on business model. Some businesses will do it explicitly, others will simply add margin to the core product.
Sure, there are some economies of scale to be had ... but in the end, it ain't cheap to run a busy e-commerce site.